[English] 日本語
Yorodumi
- PDB-4pf5: Crystal structure of Concanavalin A complexed with a synthetic de... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pf5
TitleCrystal structure of Concanavalin A complexed with a synthetic derivative of high-mannose chain
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / Lectin / High mannose
Function / homology
Function and homology information


regulation of defense response to virus / D-mannose binding / defense response / metal ion binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-M3N / : / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.04 Å
AuthorsLafite, P. / Daniellou, R.
CitationJournal: Chemistry / Year: 2015
Title: Synthesis of High-Mannose Oligosaccharide Analogues through Click Chemistry: True Functional Mimics of Their Natural Counterparts Against Lectins?
Authors: Francois-Heude, M. / Mendez-Ardoy, A. / Cendret, V. / Lafite, P. / Daniellou, R. / Ortiz Mellet, C. / Garcia Fernandez, J.M. / Moreau, V. / Djedaini-Pilard, F.
History
DepositionApr 28, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Concanavalin-A
B: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,11110
Polymers51,2452
Non-polymers8668
Water4,125229
1
A: Concanavalin-A
B: Concanavalin-A
hetero molecules

A: Concanavalin-A
B: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,22220
Polymers102,4904
Non-polymers1,73316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_444x-y-1/3,-y-2/3,-z-2/31
Buried area9860 Å2
ΔGint-64 kcal/mol
Surface area33670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.901, 125.901, 181.972
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
DetailsHomo-4-mer

-
Components

#1: Protein Concanavalin-A / Con A


Mass: 25622.385 Da / Num. of mol.: 2 / Fragment: Residues 164-281, 30-148 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Sugar ChemComp-M3N / 4-(hydroxymethyl)-1-(alpha-D-mannopyranosyl)-1H-1,2,3-triazole / 4-(hydroxymethyl)-1-(alpha-D-mannosyl)-1H-1,2,3-triazole / 4-(hydroxymethyl)-1-(D-mannosyl)-1H-1,2,3-triazole / 4-(hydroxymethyl)-1-(mannosyl)-1H-1,2,3-triazole


Type: D-saccharide / Mass: 261.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N3O6
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium Acetate, 1,4-dioxane

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2013 / Details: mirrors
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.04→93.529 Å / Num. all: 35512 / Num. obs: 35512 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 29.12 Å2 / Rpim(I) all: 0.059 / Rrim(I) all: 0.176 / Rsym value: 0.166 / Net I/av σ(I): 2.791 / Net I/σ(I): 8.2 / Num. measured all: 316169
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.04-2.158.90.5941.24593851480.2110.5943.1100
2.15-2.288.80.4191.74273248480.150.4194.2100
2.28-2.449.10.371.94146645800.1310.375.3100
2.44-2.6390.3182.13828642680.1120.3186.6100
2.63-2.8890.2412.63530739290.0850.2418.3100
2.88-3.238.90.1723.63179835670.0610.17210.8100
3.23-3.728.90.1384.22820731670.0490.13813.4100
3.72-4.568.80.1214.42376626880.0430.12115.2100
4.56-6.458.80.1144.41857721110.0410.11415.3100
6.45-46.7658.40.1024.71009212060.0380.10214.599.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.20data scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→41.985 Å / FOM work R set: 0.8359 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 1998 5.63 %
Rwork0.1781 33492 -
obs0.1808 35490 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.56 Å2 / Biso mean: 34.12 Å2 / Biso min: 16.61 Å2
Refinement stepCycle: final / Resolution: 2.04→41.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3611 0 48 229 3888
Biso mean--38.05 38.4 -
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083755
X-RAY DIFFRACTIONf_angle_d1.2125123
X-RAY DIFFRACTIONf_chiral_restr0.055592
X-RAY DIFFRACTIONf_plane_restr0.005658
X-RAY DIFFRACTIONf_dihedral_angle_d13.3371307
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.04-2.0910.28911400.210323602500
2.091-2.14760.27051420.221123812523
2.1476-2.21080.28781410.223823702511
2.2108-2.28210.25191420.20623612503
2.2821-2.36370.23231420.195823842526
2.3637-2.45830.2671410.200123602501
2.4583-2.57020.26671420.196923782520
2.5702-2.70560.2431420.191723842526
2.7056-2.87510.23391440.195223942538
2.8751-3.09710.2241400.181523672507
3.0971-3.40860.25491440.18124042548
3.4086-3.90150.2271440.16323982542
3.9015-4.91430.16731450.142424392584
4.9143-41.99390.20251490.166925122661

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more